Metadata-Version: 2.1
Name: transfacpred
Version: 1.1.1
Summary: A method to predict the transcription factors using protein sequences.
Home-page: https://github.com/raghavagps/transfacpred
Requires-Python: >=3.6
Description-Content-Type: text/markdown
License-File: LICENSE.txt

TransFacPred

A highly accurate method to predict the transcription factors using protein sequences.


## Introduction

TransFacPred is developed for predicting the transcription factors (TFs) using the protein primary sequence information. In this approach, Hybrid model was implemented in which is a combination of ET-based model and BLAST Search.


## Webserver and Standalone

Available as web-server at https://webs.iiitd.edu.in/raghava/transfacpred

Available as standalone at https://github.com/raghavagps/transfacpred/

## Installation


To install the Transfacpred package, use the following command:

```bash
pip install transfacpred
```


## Minimum USAGE

To explore the available options for the command-line tool, use:

```bash
transfacpred -h
```

## Full Usage

```bash
usage: transfacpred [-h] 
                       [-i INPUT 
                       [-o OUTPUT]
                       [-t THRESHOLD]
                       [-d {1,2}]


Please provide following arguments for successful run

optional arguments:
  -h, --help            show this help message and exit
  -i INPUT, --input INPUT
                        Input: File name containing protein or peptide sequence in FASTA format.
  -o OUTPUT, --output OUTPUT
                        Output: File for saving results by default outfile.csv
  -t THRESHOLD, --threshold THRESHOLD
                        Threshold: Value between -0.5 to 1.5 by default -0.38
  -d {1,2}, --display {1,2}
                        Display: 1:Transcription Factors, 2: All Sequences, by default 1
```


**Input File:** It allow users to provide input in the FASTA format.

**Output File:** Program will save the results in the CSV format, in case user do not provide output file name, it will be stored in "outfile.csv".

**Threshold:** User should provide threshold between -0.5 and 1.5.


**Example usage details:**

```bash
transfacpred.py -i protein.fa
```

This will predict if the submitted sequences are TFs or Non-TFs and display only the TFs. It will use other parameters by default. It will save the output in "outfile.csv"


```bash
transfacpred -i protein.fa -o output.csv -t 0.55 -d 2
```

This will predict if the submitted sequences are TFs or Non-TFs and display all. It will save the output in "output.csv" in CSV (comma seperated variables).


# Reference
Patiyal et al. (2022) A hybrid approach for predicting transcription factors. <a href="https://doi.org/10.1101/2022.07.13.499865">Bioxriv doi: https://doi.org/10.1101/2022.07.13.499865 </a> 
